VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Mar 10 2010 - 23:26:30 CST

I guess what you need is the glycerol topology? I'm pretty sure this is in
Charmm - see MacKerell's website for the full forcefield topology and
parameter set: http://mackerell.umaryland.edu/CHARMM_ff_params.html

 

 

From: Roshan Tasgaonkar [mailto:roshantaz_at_hotmail.com]
Sent: Wednesday, March 10, 2010 11:19 PM
To: gumbart_at_ks.uiuc.edu
Subject: RE: vmd-l:

 

I am familiar with running basic MD simulations, the problem i'm having is
in inputting many glycerin molecules because they are very small and its not
possible to create a psf for them which can than be solvated

 

Roshan

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From: gumbart_at_ks.uiuc.edu
To: roshantaz_at_hotmail.com; vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l:
Date: Wed, 10 Mar 2010 23:00:43 -0600

http://www.ks.uiuc.edu/Training/Tutorials

 

Try the VMD and NAMD tutorials to start.

 

 

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Roshan Tasgaonkar
Sent: Wednesday, March 10, 2010 10:56 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l:

 

Hey guys!

 

I want to run a simulation on linux where i have a insulin solvated in a box
of water with a lot of glycerins in the box. I am not sure how to start
doing this, i know how to solvate and know the basics of linux. I heard it
has something to do with .inp files? could someone outline a way for me to
be able to run this MD simulation

 

thanks

 

Roshan Tasgaonkar

 

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